Angela Smith, Minister for the Third Sector, has paid back £300 in expenses after a request from auditor Sir Thomas Legg.
Legg is going through MPs' second-home allowance claims and asking them to pay back those payments he thinks were made in error.
But Smith, the MP for Basildon, said she did not understand how she could have overclaimed for mortgage interest payments on her second home in Elephant & Castle.
"I submitted my mortgage interest claims as advised, so I don't know how I could have been paid the wrong amount," she said. "But I've refunded the £300 requested."
Smith said she had repaid the money to comply with the review and "move forward with the expenses issue".
However, about 50 MPs are contesting Legg's demand that they repay expenses.
In June, Smith paid back more than £1,000 in wrongly claimed council tax expenses and service charges for the Elephant & Castle flat.